I'm fairly certain that alignment was the cause of failure of the C.S.S. Arkansas powertrain. The prints I have read do not show a single bed supporting the engines and drive trains. The only power disconnects were on the propeller shafts. Were the alignment to go off square in this arrangement shaft binding would be a certainty. Shawn, you mention the boiler used as a structural member, certainly transferring stress to any related members.
They don't make 'em like they used to.